Dark Captain Swan
by alexandra142
Summary: My mind hasn't been at ease since the episode "Birth," so this is my take and hope on what happens next. Chapter 7 onward will be based on episode 5x10 (Broken Heart.)
1. Chapter 1

It was a dark night, the moon was brightly lit, and Emma, Hook, and Zelena stood in the living room of Emma's house. Hook was now a dark one, and all his nightmares had become true.

"This is how it's going to go," Hook started with a scowl on his face.

"I'm sorry Killian," Emma said, still paralyzed by the squid ink.

Emma couldn't escape the regret that had been eating away at her heart for weeks. She knew she'd have an angry pirate to own up to, but she couldn't lose him just like she lost Graham and Neal.

A full excalibur was in the hand of Captain Hook with the names Killian Jones and Emma Swan engraved on it. The blade shined, but Killian's face was still a scowl.

"As much as I hate you, I'm going to have to put it aside because you, Zelena, and I are going to plan something big," Killian said as he pointed Excalibur at Emma and Zelena.

"That's a wonderful idea Hook. I like my new dark one friend," Zelena said with a smile.

"So, Emma, what do you choose? Now choose wisely, because I will make sure to hurt you like you hurt me," Killian said as he walked closer to Emma.

"Please, Killian. This isn't who you are," Emma said looking into Killian's eyes.

"It's what you made me! Do you think I want to hear voices in my head, one of which is yours?" Killian yelled angrily.

"Well, I've got to get my baby dears, I'll see you soon," Zelena said as she started to walk out the door.

"Not until we work this out, now Emma, what will it be?" Killian said stopping Zelena with magic.

"Yes, but you must swear, both of you, not to harm my family." Emma said.

"Ugh, fine dear, but you're just ruining the fun," Zelena said.

"Good," Hook removed the squid ink's affects from Emma and they disappeared in a puff of dark blue smoke.

"Lovebirds," Zelena said as she disappeared in a puff of green smoke.

* * *

Zelena reappeared in the hospital with a grin on her face. Dr. Whale was still unconscious in a corner, but other then that all was peaceful. Robin Hood stood there holding Zelena and his's child, he looked at the baby girl with doe eyes. It was the baby that Zelena wished would love her and only her.

"I'll have my baby thank you," Zelena said as she poofed the baby into her arms.

The emotions of joy flooded in so quickly. The old angry baby stuck in Zelena's stomach was now free and beautiful.

"Zelena, please we can raise this child together... How do you have m-" Robin Hood started.

"Magic, o that's the benefit of having friends in this town, but I have bigger plans, I'll see you around Robin," Zelena said disappearing in another puff of green smoke.

"Zelena!" Robin Hood yelled.

* * *

"I love you Swan," Killian said.


	2. Chapter 2

Killian had teleported Emma and him to the underbelly of his ship, the Jolly Roger. It was dark at first, but in an instance all the lights were lit. Killian placed Excalibur down, and started walking back to Emma.

"I love you Swan," Hook said as he touched Emma''s arm his hook.

"I love you too Killian," Emma said as she pulled herself closer to Hook's embrace.

Their foreheads were touching and they looked at each other, and wished they could have their happy ending for forever. They stared at each other for seconds, until they couldn't help themselves. They kissed, Hook caressed Emma's face with his hook, Emma's red lips touched Killian's, and all was perfect. Even if they were evil, it didn't matter, there love would blossom even more.

"Swan, you better own up to your promises," Hook said as he took distance from Swan.

"Of course Captain, so what's your plan? Kidnap Belle? Kill the crocodile? Find Merlin?" Emma said with a sly grin.

"Aye, I plan to take my revenge on the croc as painful as it can be for him, but I also intend to find the bloody wizard," Hook said slowly.

As much as it pained Emma to see the Captain as a villain, she loved it almost as much as she hated it. Killian finally understood who she was, all the voices, and how good it felt. Emma sat down and crossed her legs and said, "Tell me captain, what's your plan?"

Killian looked at Emma and smiled.

* * *

Regina walked into Zelena's hospital room and found a sad Robin. The blanket on the bed was still messy and Dr. Whale was still in the corner.

"What happened? Where's the baby?" Regina asked concerned.

"Zelena, shsh-she took her from me and left. I don't know how she escaped, and I don't know how she has magic," Robin Hood said as he cried.

"What? How in hell did my sister get that damn bracelet off again?" Regina exclaimed in a pissed off tone. Regina started pacing and her mind was racing.

"Wait, if Zelena escaped Emma... Emma can't of let Zelena go by accident, but what's Emma up to?" Robin said furrowing his brow.

"That wicked witch must be planning something, we need to make sure this town is prepared for whatever is coming. We need to find Nimue like Merlin told us," Regina replied.

"We have to warn Mary Margret, Charming, Belle, Gold, and Henry. We must hurry," Robin stated.

They rushed out the clean hospital room. As their shoes rubbed against the ground it squeaked. Robin grabbed Regina's hand and squeezed it tightly and said, "You are a hero Regina. You are the savior."

* * *

 **Thank you so much for reading my story! I'm going to continue to keep these chapters relatively short, but I hope you guys like it so far. Please leave a review it really helps, and tell me if you want me to continue this story or any suggestions you have. Thanks! _lm1212_**


	3. Chapter 3

Killian and Emma's voice were like soft slithers of a snake. They were having fun, laughing, and enjoying each others company. They loved each other, and being able to love each other increased their bond. Emma was no longer bombarded with comments like, this isn't you or Swan, I know you can fight the darkness. Killian finally understood what it meant to be a dark one. They continued their whispers about their plan, but they couldn't stop the flirting.

Hours went by, they were dark ones, they didn't need sleep. They laid and planned out an intricate plot. They finally finished their scheming and decided to find their wicked friend. Killian picked up Excalibur, and started his work. It didn't take long to find Zelena with a locator spell, and then teleported there. Zelena held her daughter in her arms swing them slowly back and forth. She was humming a lullaby, and the baby was quietly sleeping.

"Ugh, what do you two want?" Zelena asked.

"Revenge," Killian said.

"All of us here want that, dear. What do you want from me?" Zelena clarified.

Emma and Killian explained what they were planning to do, and what Zelena need to do. Emma then said, "Don't screw this up, Zelena.'

"Well, where's my happy ending? Where's the part where I get to do whatever I want with Regina?"

"You see Zelena, you only get that if we know we can trust you, because based on my experience in Camelot, I don't trust you," Emma stated.

"I don't remember what I did in Camelot because of you, but whatever I did you deserved it," Zelena stated edging towards Emma.

"Will you shut up ladies?" Killian shouted.

"Whatever, but fine I'll do it. Please leave me alone now," Zelena said.

Emma waved her hand and disappeared in a puff of grey smoke. Killian walked slowly towards Zelena pointing the tip at her neck.

"No need to be attacking me captain," Zelena said.

"Don't screw up," Hook said before disappearing in a puff of royal blue smoke.

* * *

Emma stood in front of Mr. Gold's shop. It was already mid morning, the sky was cloudy, and it started to feel like winter. The shop was already open, so Emma walked in. The bell rung as Emma opened the door. Rumpelstiltskin and Belle stood behind the register, but as soon as Emma walked in Rumpelstiltskin grabbed for the nearest sword.

"What do you want miss Swan?" Mr. Gold said holding up the sword and pointing it at her.

"Oh come on Gold, you were the dark one, you should know that sword won't be able to do a thing," Emma said raising a hand and flinging Rumpelstiltskin across the room.

"Emma, please leave us alone. What have has Rumple ever done to you?" Belle said.

"Well he did try to trap me in a hat, planned my life, and is a voice I hear in my head constantly. You tell me, what has Rumple done to you?" Emma said getting annoyed.

Emma walked closer to Belle and said, "Lucky for him I'm not here for him."

"What?" Belle asked confused.

"Don't worry Belle, he'll get what's coming to him, but I'm here for you," Emma said as she grabbed Belle's heart.

Belle looked at Emma, but she couldn't speak. Emma's hand was still in Belle's chest, Emma's quickly pulled her hand out. She held Belle's heart and stared at the beating red heart. Belle stared in horror and said, "Why Emma, why?"

"Does it matter?" Emma said and took Belle in a grey smoke and disappeared.

* * *

 **Thank you so much for reading my story! I'm going to continue to keep these chapters relatively short, but I hope you guys like it so far. Please leave a review it really helps, and tell me if you want me to continue this story or any suggestions you have. Thanks! _lm1212_**


	4. Chapter 4

Hook knocked on the door of Mary Margret's apartment. He waited for a few seconds, and then he heard the lock on the door being unlocked. The door swung open slowly, and Henry came face to face with Hook. Henry said, "Hey Killian, where were you last night?"

Killian chuckled and said, "I was abducted by your mom, but I escaped because I removed Zelena's bracelet and she helped me free."

Wait, Zelena's free?" Henry asked.

"Yes she's free, I was going to tell you, but you're too busy talking somebody. Who's out there?" Regina said.

"It's just me love," Killian said.

Killian entered the apartment. It was clean and neat. Mary Margaret and Charming sat next to each across from Regina and Robin Hood. Mary had a cup of tea in front of her, and Charming had a cup of coffee in front of him. Regina and Robin each had a cup of water in front of them. Killian took a seat diagonally to the right of Regina, and Henry took a seat next to him. Regina said, "So we really need to know what Emma is up to. A dark one wouldn't let a powerful witch out for free by accident."

"That may have been my fault. I was abducted by Emma as well, and I made a deal with Zelena," Hook said.

"What? You don't make deals with my sister, she just breaks them," Regina exclaimed.

"I'm sorry, but I needed to stop Swan," Killian said.

"How can you stop Swan? You're just a mere pirate missing a hand with guy liner," Regina said.

"I found some squid ink Emma hid behind a painting, and I used it on her," Hook said.

"And then you just decided to leave her?" Mary Margaret inquired.

"I needed some time alone, so I went to my ship," Killian answered.

"That doesn't sound like something you'd normally do. Wouldn't you try to talk some sense into Emma?" David asked.

"I needed a break, Charming. It's hard to see the woman you love as the dark one," Hook said as he clenched his jaw.

"Do you love her?" Charming retorted.

"Of course," Killian said as he eyed Charming.

Killian walked up and left. As he exited Mary Margaret called out, "Killian wait!"

He exited the apartment and as soon as nobody could see him he disappeared in a puff of dark blue smoke.

"There's something wrong with our resident pirate. I could sense some magic on him," Regina said concerned.

"Did he lie to us?" Robin Hood questioned.

"No, I know Killian, and I know when he is lying," Henry replied.

"Are you sure about this Henry?" David said.

"Yeah, I'm sure," Henry answered.

* * *

Killian reappeared in front of Emma and Belle. They were in the basement of Emma's house. Belle laid on the ground, her back was leaned against the wall, and her head was tilted a bit to her left. Her hands were open and lose, and her hair was still perfect. The basement was dimly lit and Excalibur's stone still stood at the back of the room. Emma held Belle's heart in her hand, and as soon as she saw Hook she smiled. Hook bent down and touched cheek and said, "Beautiful job love."

Belle woke up panicked and said, "Killian, please help me. Emma took my heart, knocked out Rumple, and-"

"Don't worry Belle, you're in no trouble," Killian said calmly.

"So please, be quiet and sleep," Emma said raising the heart.

Belle immediately went into a slumber. Killian then said, "It's time for me to catch a crocodile."

"I'll see you soon," Emma replied.

* * *

 **Thank you so much for reading my story! I'm going to continue to keep these chapters relatively short, but I hope you guys like it so far. Please leave a review it really helps, and tell me if you want me to continue this story or any suggestions you have. Thanks! _lm1212_**


	5. Chapter 5

Zelena had work to do, and among the list was fixing up the house she commandeered, cast a spell, and take care of a baby that whined all day and night. Zelena was getting tired and she didn't realize how hard it would be to take care of a child. She needed a break, she needed to do something wicked, or get a babysitter. The only problem was who in this town would willingly babysit Zelena's child? Certainly not Snow, the Blue fairy, or anybody. Maybe Zelena might have to ask her sister for a favor. Zelena placed her daughter, Elle, in her crib and went off to find Regina.

Zelena found Regina in her marble office. Regina had her phone right next to her ear, but the she said, "let me call you back. I have business to attend to."

"Back up sister, or this fireball is going to hit you," Regina said as she raised her hand.

"As if that wimpy ball could do anything," Zelena said whilst putting out the fireball.

"Well, you obviously didn't come here for a lovely chat. What do you want?"

"As you may know being a mother is exhausting, and I really need a break. Will you just take care of her for a few days, but don't worry I will come back for her."

"Fine, but-" Regina started.

Elle magically appeared in Zelena's arms, and she handed Elle over to Regina as she said, "Take care of her, good bye sister. I'll see you in two days."

Zelena vanished and Regina was left confused.

* * *

The bell rang as Killian walked in Gold's shop with the gleaming and sharp Excalibur. Rumpelstiltskin jumped up, and balanced on his walking stick. "What do you want Captain?"

Killian threw a sword across the wooden floor, and said, "Shall we finish what we started?"

"We shall," Rumpelstiltskin replied.

Hook brought Rumpelstiltskin in a puff of dark blue smoke aboard the Jolly Roger. The two of them stood on top of the Jolly Roger, and their eyes were locked profusely. Killian's devilish grin went to a pissed off frown. Runple placed his left hand over his right on top of his walking stick. Rumpelstiltskim was scared out of his mind, maybe even more scared than he was fighting Merida as a bear. Killian raised Excalibur to lure Rumpelstiltskin. Rumpelstiltskin stared at the name "Killian Jones" engraved on the sword Excalibur. Rumpelstiltskin immeadiately said, "How's thins possible? How'd did you, the person who despied all dark ones become one? Most importantly h-how are there two dark ones?"

"I don't need to answer to you Crocodile. Shall we begin?" Killian said aiming Excalibur for Rumpelstiltskin's hands.

"We shall," Rumpelstiltskin said as he blocked Killian's blow.

Killian took the more aggresive stance. He swung Excalibur around his head and aimed for Rumpelstiltskin's side. Rumple immeadiately blocked, but the blows came fast, one after another. Rumple was losing, and he felt hopeless. Killian was having a wonderful time, he was playing with a hopeless man.

Killian knew he could win, but this was so fun and wonderful to have his revenge. This was for Mila, Killian would never be able to for give the crocodile for killing his wife and stealing his heart.


	6. Chapter 6

The swords being hit could be heard miles away from the Jolly Roger. Killian wanted to kill the crocodile after so many years of torment, but he knew the croc didn't deserve such a quick fate. Even one cut from Excalibur would kill Rumpelstiltskin, and he'd bleed and bleed until he'd eventually die. Killian let himself get cut by Rumpel's blade, but Killian's skin mended and healed right away. The cruel laugh that was once Rumpelstiltskin's was now Killian's. The two of them fought hard for thirty minutes, Rumpel cringing every few minutes. Killian finally said, "Getting tired old Crocodile?"

Rumpelstiltskin didn't reply, it would be a waste of breath to reply. He was old and extremely exhausted. Rumpelstiltskin blocked a few more blows, but he lost his grip on his walking stick and fell. Rumpel tried to stand, but he couldn't, he reached for his walking stick, but Killian stepped on it. "You're still the same coward," Killian taunted.

* * *

Henry, Regina, and Mary Margaret rushed to Mr. Gold's shop. Regina slammed the door open and yelled, "GOLD!"

Henry called out, "Grandma? Belle?"

The shop was ruffed up, glass was scattered on the ground and nothing was placed in the right place like Belle usually kept it. Regina and Henry searched the back, while Mary Margaret stayed at the front as she looked for any clues. Regina finally declared, "I can feel Emma's dark magic here, and there's another trace of magic, but I don't know whose it is."

"Could it be Killian's magic?" Henry asked.

"But Killian doesn't have magic.." Mary Margaret said.

"I did notice a trace on him when he came to your apartment," Regina said.

"How would Killian get dark magic?" Henry said confused.

"Are there two dark ones?" Mary Margaret said.

* * *

A memory from Camelot:

The black liquid reformed making Killian Jones. He held a straight face and Rumpelstiltskin greeted him. He said, "Hello new dark one."

"No. This can't be possible, why does it have to be the Crocodile in my head?" Killian said.

"Would you rather me be someone else?" Rumpelstiltskin said as he turned to Emma.

"Emma?"

"Yes, Killian it's me. You have to accept this is who you are," The Emma that stood in front of Killian said.

"N-no it's not you, get out of my head. I don't need dark magic."

"I guess you'd prefer me instead," the apparition said as it turned into Rumpelstiltskin.

"I don't need you, I need the real Emma. I don't need magic."

"Really? You don't want revenge that has been bugging you for centuries."

"-," Killian didn't reply.

"I can help you."

"Help me? All you are is an annoying voice in my head."

"You know you want to kill me, and I can help you."

"How?"

"The first step is to accept who you are."

"Who am I?"

"A dark one."

* * *

Emma gave back all of Killian's memories, but i pained her. Killian didn't need to be a dark one, but she could never lose him. Emma was bored and she needed something to do as she waited for Killian. She might as well play with her new toy. Emma forced Belle to do whatever she wanted, and it was fun. Emma forced Belle to make a gourmet meal, slap herself, and if she ever saw Rumpelstiltskin she'd hate him immediately.

* * *

 **Thank you so much for reading my story! I'm going to continue to keep these chapters relatively short, but I hope you guys like it so far. Please leave a review it really helps, and tell me if you want me to continue this story or any suggestions you have. Thanks! _lm1212_**


	7. Chapter 7

**The episode Broken Heart (5x10) has aired, and my heart is most definitely broken. So these chapters onward until the winter finale will be based off of episode 5x10. I've gotta say my CS heart is very broken :(. Please leave any reviews you have or any suggestions. It'll help my writers block :). _lm1212_**

 **I don't own any of OUAT and I don't own any of these characters.**

* * *

"No," Emma said as she looked up at everybody in terror.

"What?" David said.

"He's bringing them back, all of them back," Emma said rushing her words.

"Who, Swan?" Regina said.

"The dark ones, all of them. I have to talk to him, I have to see him, I need to stop him," Emma said as she disappeared in grey smoke.

"Mom, wait," Henry said, but it was too late.

* * *

The lake was misty, and disturbed by the wooden row boat that carried the previous dark ones.

"Killian! Why?" Emma screamed as she appeared in front of Killian and the previous dark ones.

"He's just doing what all dark ones are supposed to do. Something you've failed to do, Emma," Nimue sneered.

"Don't worry Emma, you'll feel the pain I did. All the people you love will be in pain, and mark my words you will be to," Killian said playfully.

"No, you won't harm my family, and if I have to kill you I will. I will always love you Killian, but I can't let you harm my family," Emma said. The savior dark one disappeared in a grey smoke.

"Don't worry Hook, you'll get your revenge, and this town will be at the knees of you," Nimue whispered as she circled Killian.

"Shall we get to work?" Killian said.

The dark one Rumpelstiltskin cackled, and the dark ones disappeared in a puff of red smoke.

* * *

"It's too late, all of them are here, and out for blood," Emma said worried.

"How did Captain dark one do that?" Regina said.

"We don't have time for chat, we need to get a protection spell going, _NOW,"_ Emma said.

"I'll go to the shop, and see if there are any ingredients you need there," Belle said as she started walking.

"I should go with you, if Killian needs any ingredients he'll go there also," Emma said as her and Belle disappeared in a grey smoke.

"I'll see what I can do in my vault. Henry, Robin will you come with me?" Regina asked.

"Yes, but what about Baby Hood, and Roland?" Robin said.

"Roland will hopefully be safe with the merry men, but if we let Zelena take care of Baby Hood she'll be the most protected," Regina answered.

"Yes, but-," Robin started.

"Robin we don't have time, but you have to think about it Zelena will take care of your daughter very well," Henry said.

"Let's go," Regina said as she, Henry, and Robin disappeared in a puff of purple smoke.

* * *

 **Thank you for reading! I will continue this portion if I get enough positive/suggestion reviews before next weeks winter finale. Please leave a review, thanks, _lm1212._**


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